Description Usage Arguments Details Value Methods References See Also Examples

`connectivity`

is an S4 generic that computes the connectivity matrix
based on the clustering of samples obtained from a model's `predict`

method.

The consensus matrix has been proposed by Brunet et al. (2004) to help
visualising and measuring the stability of the clusters obtained by
NMF approaches.
For objects of class `NMF`

(e.g. results of a single NMF run, or NMF
models), the consensus matrix reduces to the connectivity matrix.

1 2 3 4 5 6 | ```
connectivity(object, ...)
## S4 method for signature 'NMF'
connectivity(object, no.attrib = FALSE)
consensus(object, ...)
``` |

`object` |
an object with a suitable |

`...` |
extra arguments to allow extension.
They are passed to |

`no.attrib` |
a logical that indicates if attributes containing information
about the NMF model should be attached to the result ( |

The connectivity matrix of a given partition of a set of samples (e.g. given
as a cluster membership index) is the matrix *C* containing only 0 or 1
entries such that:

*
C_{ij} = 1 if sample i belongs to the same cluster as sample j, 0 otherwise*

a square matrix of dimension the number of samples in the model, full of 0s or 1s.

- connectivity
`signature(object = "ANY")`

: Default method which computes the connectivity matrix using the result of`predict(x, ...)`

as cluster membership index.- connectivity
`signature(object = "factor")`

: Computes the connectivity matrix using`x`

as cluster membership index.- connectivity
`signature(object = "numeric")`

: Equivalent to`connectivity(as.factor(x))`

.- connectivity
`signature(object = "NMF")`

: Computes the connectivity matrix for an NMF model, for which cluster membership is given by the most contributing basis component in each sample. See`predict,NMF-method`

.- consensus
`signature(object = "NMFfitX")`

: Pure virtual method defined to ensure`consensus`

is defined for sub-classes of`NMFfitX`

. It throws an error if called.- consensus
`signature(object = "NMF")`

: This method is provided for completeness and is identical to`connectivity`

, and returns the connectivity matrix, which, in the case of a single NMF model, is also the consensus matrix.- consensus
`signature(object = "NMFfitX1")`

: The result is the matrix stored in slot ‘consensus’. This method returns`NULL`

if the consensus matrix is empty.See

`consensus,NMFfitX1-method`

for more details.- consensus
`signature(object = "NMFfitXn")`

: This method returns`NULL`

on an empty object. The result is a matrix with several attributes attached, that are used by plotting functions such as`consensusmap`

to annotate the plots.See

`consensus,NMFfitXn-method`

for more details.

Brunet J, Tamayo P, Golub TR and Mesirov JP (2004). "Metagenes and molecular pattern discovery using matrix factorization." _Proceedings of the National Academy of Sciences of the United States of America_, *101*(12), pp. 4164-9. ISSN 0027-8424, <URL: http://dx.doi.org/10.1073/pnas.0308531101>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/15016911>.

1 2 3 4 5 6 7 8 9 10 11 | ```
#----------
# connectivity,ANY-method
#----------
# clustering of random data
h <- hclust(dist(rmatrix(10,20)))
connectivity(stats::cutree(h, 2))
#----------
# connectivity,factor-method
#----------
connectivity(gl(2, 4))
``` |

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